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Forum: Bioinformatics 10-24-2013, 08:00 AM
Replies: 0
Views: 1,199
Posted By zshuhua
How does Tophat balance read-mismatches with seqment-mismatches?

Hello,
I'm using Tophat v 2.05 to map 75 bases single end reads generated by Illumina Hi-seq2000. I set segment-length with 25 as default and want to maximum mismatches of 3 allowed for each read....
Forum: Introductions 05-10-2013, 07:28 AM
Replies: 3
Views: 2,750
Posted By zshuhua
Thanks for your help! I intend to calculate...

Thanks for your help!
I intend to calculate genes/transcripts expression levels. Do I have to cut the 5' 10 bp?
I'm wondering what causes the patterns of for GGGGG, AAAAA and TCTTC, because I saw...
Forum: Bioinformatics 05-09-2013, 08:44 AM
Replies: 25
Views: 6,312
Posted By zshuhua
Hi, So, all the barcodes are NOT included in...

Hi,
So, all the barcodes are NOT included in the read sequences but only in their IDs. We only need to trim adapters but not barcodes.
Forum: Introductions 05-09-2013, 06:53 AM
Replies: 3
Views: 2,750
Posted By zshuhua
FastQC: odd kmer content

Hi,
I'm checking the data quality using fastqc for the Illumina Hi-Seq2000 reads and got odd kmer patterns (see attachment). Although an old thread suggested that 5' pattern is common, I want to...
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